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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

Basic information

species Vitis vinifera
transcript Vv17s0000g00240.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                     | |   ||  | | |  | |    |||| |   ||   ||  ||  ||   | | ||| |    || | | |  |    || |  |     |||   | |||  ||| | |||||||| || |||||||| ||||| ||||||||||| |||||||| ||||| |||||| |||| ||||| ||| | |||||||||||||| ||||
----------------------------------ggcaatagcttacgttctgcatgcg--gcttgtcaactttggacatt-gtacattatccaatt----tgaaataa--atcaatattgtgccctcatccctt-ttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 13
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacaga-atttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                | || | | |||  | | |  | || |  ||   || ||  | |  ||||  |||    || ||    |||| |  |        ||||  || |   | | || |    ||| |||| ||||| || || |||||||| ||||| ||||| |||||||| || || ||||| || || ||||||||||  | |||| | ||||||||||| |
-------------------------------ttaaaaagtatttctgccctgtagagtactgccagttttcccctggcattttctaa---ttgaaa---gtatgcatagga-----ttaattggact---tgacatttgctgcagACATTTAATGGCAAGAAATGGGAGAAATTCAATAGTGAAAAGGTGGCGTCGCTCGCATACGCCCGGATTCAAGGAAGGAGTGCTTTGATTGCTCATTTTC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
-----------gttagaatccatgcattg-taatataattatacttaatacttttttcggctttca--aaggaaagcttcttgtc---tacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaat-gtatcat-atatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
            ||  |||  | | | || || |  | | ||    | |  |    | | ||||    ||   |     |||| |   |    | ||| ||||  | | |  ||    || ||   ||  |||||  | ||    | |  | || |||  ||| | || ||||||||||||||||||||||| |||||||||||||||||||| ||||| |||||| |||| ||||| ||||| ||||| |||||||||||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggct----tgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-------------gttagaatccatgc-attgta--atataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactg--atatggac-tgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
               |  |||   ||| | ||||   |  | ||||   || |     ||| |     |  |  |  ||||      |    | ||  ||||  | | || |||  | |||||  || |   | || | |  | | | ||||   |||  |||   || ||||||||||||||||||||||| |||||||||||||||||||| ||||| |||||  |||| ||||| ||||| || || |||||||||||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttat-atggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagct-attttttcat-cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaagg--aaagcttcttgtctacaga-atttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                               | ||   ||||  ||| ||||   |  |   |   |||||||     | ||  ||    |  | | ||     ||    ||   ||| | | | |  ||| ||||  |||| |||| ||||||||| |||||||||||||| ||||| || ||||| |||||| |||| ||||||||| | |||||  ||||||||||||
--------------------------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaa--tagaaatggaaggagtataaaaatgaagaactttaacacatc-tgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaag-gaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                    ||  ||  |  ||    |    || | ||    ||      || |  ||   || |    |    || |  || ||   | | | |   |  |   |  | | |  ||| ||||||| || || || |||||||||||||| |||||||| |||||||| ||||| || ||  |||| || ||||  |  ||| | |||||||||||||
-----------------------------------gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgt-gcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 9
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaattt-cataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
              |||   | |   ||||   |||||||  |||     |  ||      |    |||  | | || ||    | |    |     |  || |   ||| |     ||   |  |  ||    |||||  |||||| ||  |||| ||||| |||||||||||||||||||| ||||| |||   || || ||||| ||||||||||||||| |||||||||||||||||||||
-----------gttatttggaaacccttatg--taatactaatttga---tataattatctgtgatttgaattctgagttcatctgattctttttgtttctaagagttgata-----tatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 11
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatg--tatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
           |   ||| || ||  ||||   |||||||         ||| | |  |     | |  |||    | | | |     ||||   ||  |     || |||  |  ||  |  |||   ||    ||||| ||||||| ||  |||| ||||| |||||||| ||||||||||| ||||| ||    || || ||||| ||||||||||||||| ||||||||||||||||||| |
----------gttagttggaa-atccttatg--taatact-------aatttgatataattatctgtgatctg--aattctgagttcatctgattctttttgtttctaagagtttatatgcctaataattaaggaatattgcacagGCTTTTCATGGGAAAAAATGGGAGAAATTCAACAGTGAAAAGGTAGCGGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTTC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                             |  ||   | ||| ||  |||||        ||||   | | |||      |  |  | ||     || || | ||  ||      ||||  | |       | || |||  ||||| ||  |||| ||||| ||||||||||| || ||||| || || || || ||||| ||||| |||||||||||||||  | ||||||||||||||||||
----------------------------gttgtttggattttcttatgcttt-------gagctatctatgtactatgaattttgggttc-----ctcatgttgatggaa-----ctaaataaag------aaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA04G37810.1 (Glycine max), 3'ss of exon 11
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaattt-cataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
              |||   | |   ||||   |||||||  |||     |  ||      |    |||  | | || ||    | |    |     |  || |   ||| |     ||   |  |  ||    |||||  |||||| ||  |||| ||||| |||||||||||||||||||| ||||| |||   || || ||||| ||||||||||||||| |||                  
-----------gttatttggaaacccttatg--taatactaatttga---tataattatctgtgatttgaattctgagttcatctgattctttttgtttctaagagttgata-----tatctaatagATAAGGAATATTGTACAGGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTG------------------

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                   |||   |||    ||||  | |   |  || | ||  |     | ||||  | |||  |    | | |||   | | |   |  | | || || | | |   || |||||||||||| ||||| || ||||| ||||||||||| |||||||||||||| |||||||||| ||| ||||| || ||| | ||||||||||| |||||||
---------------------------------gtataagctttgtacctttttatgatcaatttgt-gtagatgatgtatcatt-gttctttagaaaaaaaggaa-aaaagcgtttggttacaa-gtttaaaac-cttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                                        | | ||  || | |        |||| || ||  |    |   |  |||  ||| | ||   |  ||    ||  | |   |||||||||||| ||||| ||||||||||| |||||||| || |||||||||||| | ||| | |||||||| || ||||| ||||| ||||||||||| |||||||
--------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtccttttggga--gagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                                                                       || ||  || | | |   ||  |   |||  ||        ||  |  || | |||| | |||||||| || |||||||||||||||||||| |||||||| || ||||| || || |||||||| ||||| ||   ||| ||  | || |||||||
---------------------------------------------------------------------------------------gtttgacaccgttgttttcttcg---tgcgcatt----ctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                                             | |   |||  | | |     |  || | | |    ||  |||    | ||||  | ||         || |   |||||||| | |||||||| || || ||||||||||| ||||| |||||||||||||| || || || || || || ||||| ||  | || || || || || ||||
-------------------------------------------------------------gttctctgtgaa-aaagagagaggagattttcctacgacttggttctaaaacttgtcat---------tctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC

upper sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ29693 (Selaginella moellendorffii), 3'ss of exon 10
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                                                                                       || ||  || | | |   ||  |   |||  ||        ||  |  || | |||| | |||||||| || ||||||||||| |||||||| |||||||| || ||||| || || |||||||| ||||| ||   ||| ||  | || |||||||
---------------------------------------------------------------------------------------gtttgacaccgttgttttcttcg---tgcgcatt----ctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAATTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|33404602|gb|CF210229.1|CF210229
EST:     ATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG                         GCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCT
genomic: ATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAGgttagaatcc ... tatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCT
EST: gi|110376881|gb|EC941957.1|EC941957
EST:     ATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG                         GCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCT
genomic: ATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAGgttagaatcc ... tatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCT
EST: gi|161716528|gb|FC065225.1|FC065225
EST:     ATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAG                         GCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCT
genomic: ATGCTTTTGTCAACATGATTGATCCTCTTCATATTGTTCCATTCCATCAGgttagaatcc ... tatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
                        tgctaat  putative branch site (score: 2)
                                  aatgtatcatatattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA